Journal
NUCLEIC ACIDS RESEARCH
Volume 50, Issue 6, Pages 3475-3489Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkac144
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Funding
- United States Food and Drug Administration [HHSF223201510104C]
- Medical Research Council, UK [MR/R020566/1]
- NIH [HG010053]
- Oxford Nanopore Technologies [SC20130149]
- Associazione Italiana per la Ricerca sul Cancro [IG22851]
- Medical Research Council [MR/R020566/1]
- U.S. Food and Drug Administration [HHSF223201510104C]
- National Institutes of Health [HG010053]
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The researchers used a new technique called NRCeq to identify the complete subgenomic RNAs of the SARS-CoV-2 virus and annotate the capping sites in the viral genome. They successfully obtained robust estimates of subgenomic RNA expression in cell lines and viral isolates, and discovered novel subgenomic RNA variants. These findings are of great importance to the scientific community.
The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5 ' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
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